Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate SM_b20891 SM_b20891 dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Smeli:SM_b20891 Length = 477 Score = 361 bits (926), Expect = e-104 Identities = 195/475 (41%), Positives = 283/475 (59%), Gaps = 14/475 (2%) Query: 7 LADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGS 66 +A +W+ G G +INP++ D V+ + + +D K AI A A F WSR+ +R + Sbjct: 8 IAGEWVGGDG--VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65 Query: 67 ILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSA 126 IL K + + E L++ EEGKTL + + E R+ + +F+ +++G+ +PS Sbjct: 66 ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSV 125 Query: 127 DPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVE 186 P + +EP GVV +ITPWNFP++IP WKLAPAL GNT V KPA P +V+ Sbjct: 126 RPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVD 185 Query: 187 VLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRI 246 +L +AGLP+GV+NLV+GKGS VG ++ ++ A++FTGST GKR+ NR + Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNR--KY 243 Query: 247 QLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLER 306 QLE+GGKN V ADL++A E AV F TGQ CTA+SR+I+ + ++ +F + ER Sbjct: 244 QLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGER 303 Query: 307 VKKWRVG----PGTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYF 360 +K V PGT +GPVVD+ Q +D +YI GK GAKL +GG +I G++ Sbjct: 304 IKGLVVDDALKPGTH---IGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFY 360 Query: 361 LEPTIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAIN 420 L+P +F T++MR+ +EEIFGPV +V KD DEA+ + N +G ++GI + +K Sbjct: 361 LQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHAT 420 Query: 421 EFVSRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 F EAG++ VN PT G++ PFGG K S +E G+ A EFY KT Y Sbjct: 421 HFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGP-REQGKYAAEFYTNVKTAY 474 Lambda K H 0.316 0.135 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 642 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 477 Length adjustment: 34 Effective length of query: 444 Effective length of database: 443 Effective search space: 196692 Effective search space used: 196692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory